Simplify calculate_interaction_scores()

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -215,7 +215,7 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
       WT_sd_r = sd_r,
       WT_sd_AUC = sd_AUC
     ) %>%
-    group_by(across(all_of(group_vars)), conc_num, conc_num_factor) %>%
+    group_by(OrfRep, Gene, num, conc_num, conc_num_factor) %>%
     mutate(
       N = sum(!is.na(L)),
       NG = sum(NG, na.rm = TRUE),
@@ -229,18 +229,20 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
         sd = ~sd(., na.rm = TRUE),
         se = ~ifelse(sum(!is.na(.)) > 1, sd(., na.rm = TRUE) / sqrt(sum(!is.na(.)) - 1), NA)
       ), .names = "{.fn}_{.col}")
-    )
+    ) %>%
+    ungroup()
 
   stats <- stats %>%
+    group_by(OrfRep, Gene, num) %>%
     mutate(
-      Raw_Shift_L = mean_L[[1]] - bg_means$L,
-      Raw_Shift_K = mean_K[[1]] - bg_means$K,
-      Raw_Shift_r = mean_r[[1]] - bg_means$r,
-      Raw_Shift_AUC = mean_AUC[[1]] - bg_means$AUC,
-      Z_Shift_L = Raw_Shift_L[[1]] / bg_sd$L,
-      Z_Shift_K = Raw_Shift_K[[1]] / bg_sd$K,
-      Z_Shift_r = Raw_Shift_r[[1]] / bg_sd$r,
-      Z_Shift_AUC = Raw_Shift_AUC[[1]] / bg_sd$AUC
+      Raw_Shift_L = first(mean_L) - bg_means$L,
+      Raw_Shift_K = first(mean_K) - bg_means$K,
+      Raw_Shift_r = first(mean_r) - bg_means$r,
+      Raw_Shift_AUC = first(mean_AUC) - bg_means$AUC,
+      Z_Shift_L = first(Raw_Shift_L) / bg_sd$L,
+      Z_Shift_K = first(Raw_Shift_K) / bg_sd$K,
+      Z_Shift_r = first(Raw_Shift_r) / bg_sd$r,
+      Z_Shift_AUC = first(Raw_Shift_AUC) / bg_sd$AUC
     )
 
   stats <- stats %>%
@@ -270,111 +272,81 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
       Zscore_K = Delta_K / WT_sd_K,
       Zscore_r = Delta_r / WT_sd_r,
       Zscore_AUC = Delta_AUC / WT_sd_AUC
-    ) %>%
-    ungroup()
-
-  # Create linear models with error handling for missing/insufficient data
-  # This part is a PITA so best to contain it in its own function
-  calculate_lm_values <- function(y, x) {
-    if (length(unique(x)) > 1 && sum(!is.na(y)) > 1) {
-      # Suppress warnings only for perfect fits or similar issues
-      model <- suppressWarnings(lm(y ~ x))
-      coefficients <- coef(model)
-      r_squared <- tryCatch({
-        summary(model)$r.squared
-      }, warning = function(w) {
-        NA  # Set r-squared to NA if there's a warning
-      })
-      return(list(intercept = coefficients[1], slope = coefficients[2], r_squared = r_squared))
-    } else {
-      return(list(intercept = NA, slope = NA, r_squared = NA))
-    }
-  }
-
-  lms <- stats %>%
-    group_by(across(all_of(group_vars))) %>%
-    reframe(
-      lm_L = list(calculate_lm_values(Delta_L, conc_num_factor)),
-      lm_K = list(calculate_lm_values(Delta_K, conc_num_factor)),
-      lm_r = list(calculate_lm_values(Delta_r, conc_num_factor)),
-      lm_AUC = list(calculate_lm_values(Delta_AUC, conc_num_factor))
     )
 
-  lms <- lms %>%
-    mutate(
-      lm_L_intercept = sapply(lm_L, `[[`, "intercept"),
-      lm_L_slope = sapply(lm_L, `[[`, "slope"),
-      lm_L_r_squared = sapply(lm_L, `[[`, "r_squared"),
-      lm_K_intercept = sapply(lm_K, `[[`, "intercept"),
-      lm_K_slope = sapply(lm_K, `[[`, "slope"),
-      lm_K_r_squared = sapply(lm_K, `[[`, "r_squared"),
-      lm_r_intercept = sapply(lm_r, `[[`, "intercept"),
-      lm_r_slope = sapply(lm_r, `[[`, "slope"),
-      lm_r_r_squared = sapply(lm_r, `[[`, "r_squared"),
-      lm_AUC_intercept = sapply(lm_AUC, `[[`, "intercept"),
-      lm_AUC_slope = sapply(lm_AUC, `[[`, "slope"),
-      lm_AUC_r_squared = sapply(lm_AUC, `[[`, "r_squared")
-    ) %>%
-    select(-lm_L, -lm_K, -lm_r, -lm_AUC)
-
   stats <- stats %>%
-    left_join(lms, by = group_vars) %>%
     mutate(
-      lm_Score_L = lm_L_slope * max_conc + lm_L_intercept,
-      lm_Score_K = lm_K_slope * max_conc + lm_K_intercept,
-      lm_Score_r = lm_r_slope * max_conc + lm_r_intercept,
-      lm_Score_AUC = lm_AUC_slope * max_conc + lm_AUC_intercept,
-      R_Squared_L = lm_L_r_squared,
-      R_Squared_K = lm_K_r_squared,
-      R_Squared_r = lm_r_r_squared,
-      R_Squared_AUC = lm_AUC_r_squared,
       Sum_Zscore_L = sum(Zscore_L, na.rm = TRUE),
       Sum_Zscore_K = sum(Zscore_K, na.rm = TRUE),
       Sum_Zscore_r = sum(Zscore_r, na.rm = TRUE),
       Sum_Zscore_AUC = sum(Zscore_AUC, na.rm = TRUE)
     )
 
+  # Calculate linear models and store in own df for now
+  lms <- stats %>%
+    reframe(
+      L = lm(Delta_L ~ conc_num_factor),
+      K = lm(Delta_K ~ conc_num_factor),
+      r = lm(Delta_r ~ conc_num_factor),
+      AUC = lm(Delta_AUC ~ conc_num_factor)
+    )
+
   stats <- stats %>%
     mutate(
       Avg_Zscore_L = Sum_Zscore_L / num_non_removed_concs,
       Avg_Zscore_K = Sum_Zscore_K / num_non_removed_concs,
       Avg_Zscore_r = Sum_Zscore_r / (total_conc_num - 1),
       Avg_Zscore_AUC = Sum_Zscore_AUC / (total_conc_num - 1),
+      lm_Score_L = max_conc * coef(lms$L)[2] + coef(lms$L)[1],
+      lm_Score_K = max_conc * coef(lms$K)[2] + coef(lms$K)[1],
+      lm_Score_r = max_conc * coef(lms$r)[2] + coef(lms$r)[1],
+      lm_Score_AUC = max_conc * coef(lms$AUC)[2] + coef(lms$AUC)[1],
+      R_Squared_L = summary(lms$L)$r.squared,
+      R_Squared_K = summary(lms$K)$r.squared,
+      R_Squared_r = summary(lms$r)$r.squared,
+      R_Squared_AUC = summary(lms$AUC)$r.squared
+    )
+
+  stats <- stats %>%
+    mutate(
       Z_lm_L = (lm_Score_L - mean(lm_Score_L, na.rm = TRUE)) / sd(lm_Score_L, na.rm = TRUE),
       Z_lm_K = (lm_Score_K - mean(lm_Score_K, na.rm = TRUE)) / sd(lm_Score_K, na.rm = TRUE),
       Z_lm_r = (lm_Score_r - mean(lm_Score_r, na.rm = TRUE)) / sd(lm_Score_r, na.rm = TRUE),
       Z_lm_AUC = (lm_Score_AUC - mean(lm_Score_AUC, na.rm = TRUE)) / sd(lm_Score_AUC, na.rm = TRUE)
-    ) %>%
-    ungroup()
+    )
 
   # Declare column order for output
   calculations <- stats %>%
-    select("OrfRep", "Gene", "num", "conc_num", "conc_num_factor",
-           "mean_L", "mean_K", "mean_r", "mean_AUC",
-           "median_L", "median_K", "median_r", "median_AUC",
-           "sd_L", "sd_K", "sd_r", "sd_AUC",
-           "se_L", "se_K", "se_r", "se_AUC",
-           "Raw_Shift_L", "Raw_Shift_K", "Raw_Shift_r", "Raw_Shift_AUC",
-           "Z_Shift_L", "Z_Shift_K", "Z_Shift_r", "Z_Shift_AUC",
-           "WT_L", "WT_K", "WT_r", "WT_AUC",
-           "WT_sd_L", "WT_sd_K", "WT_sd_r", "WT_sd_AUC",
-           "Exp_L", "Exp_K", "Exp_r", "Exp_AUC",
-           "Delta_L", "Delta_K", "Delta_r", "Delta_AUC",
-           "Zscore_L", "Zscore_K", "Zscore_r", "Zscore_AUC",
-           "NG", "SM", "DB")
+    select(
+      "OrfRep", "Gene", "num", "conc_num", "conc_num_factor",
+      "mean_L", "mean_K", "mean_r", "mean_AUC",
+      "median_L", "median_K", "median_r", "median_AUC",
+      "sd_L", "sd_K", "sd_r", "sd_AUC",
+      "se_L", "se_K", "se_r", "se_AUC",
+      "Raw_Shift_L", "Raw_Shift_K", "Raw_Shift_r", "Raw_Shift_AUC",
+      "Z_Shift_L", "Z_Shift_K", "Z_Shift_r", "Z_Shift_AUC",
+      "WT_L", "WT_K", "WT_r", "WT_AUC",
+      "WT_sd_L", "WT_sd_K", "WT_sd_r", "WT_sd_AUC",
+      "Exp_L", "Exp_K", "Exp_r", "Exp_AUC",
+      "Delta_L", "Delta_K", "Delta_r", "Delta_AUC",
+      "Zscore_L", "Zscore_K", "Zscore_r", "Zscore_AUC",
+      "NG", "SM", "DB")
     
   interactions <- stats %>%
-    select("OrfRep", "Gene", "num", "Raw_Shift_L", "Raw_Shift_K", "Raw_Shift_AUC", "Raw_Shift_r",
-           "Z_Shift_L", "Z_Shift_K", "Z_Shift_r", "Z_Shift_AUC",
-           "lm_Score_L", "lm_Score_K", "lm_Score_AUC", "lm_Score_r",
-           "R_Squared_L", "R_Squared_K", "R_Squared_r", "R_Squared_AUC",
-           "Sum_Zscore_L", "Sum_Zscore_K", "Sum_Zscore_r", "Sum_Zscore_AUC",
-           "Avg_Zscore_L", "Avg_Zscore_K", "Avg_Zscore_r", "Avg_Zscore_AUC",
-           "Z_lm_L", "Z_lm_K", "Z_lm_r", "Z_lm_AUC",
-           "NG", "SM", "DB") %>%
+    select(
+      "OrfRep", "Gene", "num", "Raw_Shift_L", "Raw_Shift_K", "Raw_Shift_AUC", "Raw_Shift_r",
+      "Z_Shift_L", "Z_Shift_K", "Z_Shift_r", "Z_Shift_AUC",
+      "lm_Score_L", "lm_Score_K", "lm_Score_AUC", "lm_Score_r",
+      "R_Squared_L", "R_Squared_K", "R_Squared_r", "R_Squared_AUC",
+      "Sum_Zscore_L", "Sum_Zscore_K", "Sum_Zscore_r", "Sum_Zscore_AUC",
+      "Avg_Zscore_L", "Avg_Zscore_K", "Avg_Zscore_r", "Avg_Zscore_AUC",
+      "Z_lm_L", "Z_lm_K", "Z_lm_r", "Z_lm_AUC",
+      "NG", "SM", "DB") %>%
     arrange(desc(lm_Score_L)) %>%
     arrange(desc(NG))
 
+  print(df, n = 1)
+  print(calculations, n = 1)
   df <- df %>% select(-any_of(setdiff(names(calculations), group_vars)))
   df <- left_join(df, calculations, by = group_vars)
   # df <- df %>% select(-any_of(setdiff(names(interactions), group_vars)))